I do not know anything about your relationship with your wife, so I apologize in advance for being presumptious.
We had similar problems with our boys and we found that it was the relationship between my wife and I that was the problem, not the children.
I would come home from work and give my wife a kiss and then spend time with my boys. We would wrestle and play games and color. All of the things that I had looked forward to when I became a daddy. Then the late nights started. My boys had always been good sleepers so right away I suspected something serious like an illness or growning pains. None of those seemed to be the cause of the problem.
Through a parenting course that we began taking, we learned that the most important relationship in the family is the husband/wife relationship. No big surprise to us, we had a very good relationship. Once the boys would go to be, we would enjoy time together talking about our days and books that we would read together. So to hear that, was not a big surprise. The next thing they pointed out was that children need security. They need to know that mommy and daddy love each other. Not only do they need to know it, they need to see it. Have you ever noticed how when the husband/wife relationship starts to have struggles, the 3-year old's behaviors begin to change. They have something innate built into them that causes them to know that when something is not right with mommy and daddy, I need to fix it.
To attempt to resolve this, my wife and I instituted "Couch Time". All is entailed was 10-15 minutes of time spent together, in plain view of our children. I now come home from work, give everyone hugs, kisses, etc... Then, I announce to my boys that I am going to spend some time with their mommy. I tell them that the relationship between their mother and I is the most precious thing to me. It is because of that relationship, that I am able to have an even better relationship with them. I let them know that they are to play with their toys while mommy and daddy spend time together. Unless there is an emergency, we should not be interupted. We then spend our time together, right in front of the boys.
The first couple of nights were a little rocky. Constant interruptions and distractions, but they soon subsided when they realized that this was going to be a daily routine. We changed nothing else in their lives as far as diet, nap times, bed time rituals, etc.. But within 5 nights, both of my boys went back to sleeping through the night.
Durring our parenting class, i had mentioend that we were having issues with our boys getting up at night and coming into our room. They suggested couch time to us and said that if it was not a physical issue with the boys, that this should solve the problem. To be honest, I laughed at the idea. I thought, how could something so corny, that is done around 6:00, have anything to do with what happens to my boys at 1:30 in the morning. Well, I have always enjoyed the taste of good crow

Here is a link to another site that talks about couch time:
http://www.marriedadults.com/couchtime.php